Command line Training Set First Motif Summary of Motifs Termination Explanation


Search sequence databases with these motifs using
MAST.
Submit these motifs to BLOCKS multiple alignment processor.
Build and use a motif-based hidden Markov model (HMM) using Meta-MEME.


MEME - Motif discovery tool

MEME version 3.0 (Release date: 2002/03/22 05:58:46)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu.

This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.sdsc.edu.


REFERENCE

If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.


TRAINING SET

DATAFILE= INO_up800.s
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
CHO1                     1.0000    800  CHO2                     1.0000    800  
FAS1                     1.0000    800  FAS2                     1.0000    800  
ACC1                     1.0000    800  INO1                     1.0000    800  
OPI3                     1.0000    800  


COMMAND LINE SUMMARY

This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme INO_up800.s -mod tcm -dna -revcomp -bfile yeast.nc.6.freq -nmotifs 3 

model:  mod=           tcm    nmotifs=         3    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           50    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=       35    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            5600    N=               7
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.304 C 0.196 G 0.196 T 0.304 
Background letter frequencies (from yeast.nc.6.freq):
A 0.324 C 0.176 G 0.176 T 0.324 


P N
MOTIF 1
    width = 15     sites = 14     llr = 174     E-value = 2.3e-003

SimplifiedA:::8:a:::442411
pos.-specificC:1a19:117527644
probabilityG:::1:::83:4:11:
matrixTa9:11:91:111:44
.
bits 2.5 
2.3 
2.0 
1.8   
Information 1.5      
content 1.3         
(17.9 bits)1.0          
0.8            
0.5              
0.3               
0.0
.
Multilevel TTCACATGCCACCCC
consensus GAGAATT
sequence C
.
NAME STRAND START P-VALUE    SITES
 
FAS1+956.14e-09 GGCCAAAAACTTCACATGCCGCCCAGCCAAGCATA
INO1-6172.63e-08 GACAATACTTTTCACATGCCGCATTTAGCCGCCGA
FAS2+5671.80e-07 CTCCCGCGTTTTCACATGCTACCTCATTCGCCTCG
CHO1+6112.03e-07 ACTTTGAACGTTCACACGGCACCCTCACGCCTTTG
ACC1+834.22e-07 CGTTAAAATCTTCACATGGCCCGGCCGCGCGCGCG
CHO2+3545.33e-07 TGCCACACTTTTCTCATGCCGCATTCATTATTCGC
CHO1+6407.59e-07 CCTTTGAGCTTTCACATGGACCCATCTAAAGATGA
INO1-5688.34e-07 CTCCGCATATTTCACATTCAACACTTTCGATTCCG
OPI3+6371.02e-06 CTTTTCAATCTTCATATGCAAACCCACACATGCAT
INO1+6871.10e-06 ACTTATTTAATTCACATGGAGCAGAGAAAGCGCAC
OPI3-5821.84e-06 GGTGCAACTTTCCACATGCACTCTCATTGACACCT
INO1-5472.76e-06 CACTTTCGATTCCGCATCCAACCCCGGAACACCGG
CHO1+1633.42e-06 TCTGGCGCCCTTCCCATTCCGAACCATGTTATATT
CHO2-4787.37e-06 AATCTGTATTTTCATATGCCTACTTATAAATTCAC


Motif 1 block diagrams

NameLowest
p-value
   Motifs
FAS1 6.1e-09

+1
INO1 2.8e-06

-1
-1
-1
+1
FAS2 1.8e-07

+1
CHO1 7.6e-07

+1
+1
+1
ACC1 4.2e-07

+1
CHO2 5.3e-07

+1
-1
OPI3 1e-06

-1
+1
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775


Motif 1 in BLOCKS format


to BLOCKS multiple alignment processor.


Motif 1 position-specific scoring matrix


Motif 1 position-specific probability matrix






Time 180.12 secs.


P N
MOTIF 2
    width = 21     sites = 8     llr = 133     E-value = 1.8e+000

SimplifiedA:3::5:53:44:5:::::11:
pos.-specificC:149391:9:46193::93:8
probabilityGa44111::14311:3a41643
matrixT:33:1:48:3:3315:6::5:
.
bits 2.5  
2.3  
2.0      
1.8        
Information 1.5        
content 1.3        
(24.0 bits)1.0           
0.8             
0.5                 
0.3                    
0.0
.
Multilevel GGCCACATCAACACTGTCGTC
consensus AGCTAGCTTCGCGG
sequence TTTGG
.
NAME STRAND START P-VALUE    SITES
 
INO1-3668.00e-12 TGTCCATCAAGGGCACATCGGCACCGGCCTCATCGTCTTCA
FAS2+7132.52e-10 GGTTACACAAGACCACATCACCACTGTCGTGCTTTTCTAAT
OPI3-5011.97e-09 ATTATACGGCGGCGCCATCACTACTGTCGTCCCACCTGGGT
FAS1+531.67e-08 TGCAGGCACGGTTCACTACTCCCCTGGCCTCCAACAAACGA
INO1+7061.97e-08 AGCAGAGAAAGCGCACCTCTGCGTTGGCGGCAATGTTAATT
ACC1-532.31e-08 AGATTTTAACGGGCGCAACGATTCGGTGGGCAGTGGAAATT
OPI3+2929.79e-08 CCATTTGGTGGTCCCGTTCAACTCCGTCAGGTCTTCCACGT
OPI3-3542.00e-07 CATTATCGTGGATCTCTTGGAGACGGTCGACAAGAGCGATC


Motif 2 block diagrams

NameLowest
p-value
   Motifs
INO1 2e-08

-2
+2
FAS2 2.5e-10

+2
OPI3 2e-07

+2
-2
-2
FAS1 1.7e-08

+2
ACC1 2.3e-08

-2
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775


Motif 2 in BLOCKS format


to BLOCKS multiple alignment processor.


Motif 2 position-specific scoring matrix


Motif 2 position-specific probability matrix






Time 348.90 secs.


P N
MOTIF 3
    width = 29     sites = 13     llr = 201     E-value = 4.5e+002

SimplifiedA:1::22521::2:12:251::11:61:22
pos.-specificC:::252:5:::252:521235::8:2158
probabilityG::51111:62:22:3223212:222471:
matrixTa958355338a548544156398:2323:
.
bits 2.5
2.3
2.0
1.8 
Information 1.5    
content 1.3        
(22.3 bits)1.0          
0.8                 
0.5                     
0.3                            
0.0
.
Multilevel TTTTCTACGTTTCTTCTATTCTTCAGGCC
consensus GTATTTCTGTAGCCTGTTTTA
sequence AACC
.
NAME STRAND START P-VALUE    SITES
 
INO1+4904.38e-13 ATTATTGCCTTTTTCTTCGTTCCTTTTGTTCTTCACGTCCTTTTTATGA
FAS1+3532.83e-10 CTCCAAACACTTTTCCTTTTTCCTTCTATTCTGCAGGACCAACTAAAAC
FAS2+3859.52e-09 CTTTACTATATTTCCTAAATTTTCTCTGGTCTGCAGGCCAAAAACAACA
INO1+6371.86e-08 GTGAAAAGTATTGTCTATTTTATCTTCATCCTTCTTTCCCAGAATATTG
FAS2-1772.03e-08 AATCTTGTTCTTTCTTGCTTTTCTGGCACTCTTGACGGCTTTATCGGTA
ACC1+2692.23e-08 ACTGTCACAATTGTTATCGGTTCTACAATTGTTCTGCTCTCTTCAATTT
INO1+933.48e-08 GGACGACTTGTTGTTAATGGTTTTGGCGGTTTTCATTCCCCCAGTGGCC
FAS2+2444.50e-08 TTCGCCATCATTGTAGTCGTTGTTGTTGTCGTTGTTGTCCCAGCCGTTG
FAS2-106.80e-08 CTGCCATGGATTTTTCTAGTTTCAATAACTCTTGGTGCCTTGCCTGGA
INO1+2457.98e-08 ATGAAACGAGTAGTGAACGTTCGTACGATCTTTCACGCAGACATGCGAC
ACC1-7571.27e-07 AAACTTGATTTTTTCTAATTTTCTGCGCTGTTTCGGGAACGGAAAAAAA
ACC1-3491.37e-07 AATTAGGGAATTGGCTTTGTTGTTTTTTATCTTCAGGTAAACTGTACGA
CHO2+6541.86e-06 TATCCCCTAATTTTATACGTTAGTTCAACCTAACAATCCAGGATTTCAT


Motif 3 block diagrams

NameLowest
p-value
   Motifs
INO1 1.9e-08

+3
+3
+3
+3
FAS1 2.8e-10

+3
FAS2 6.8e-08

-3
-3
+3
+3
ACC1 1.4e-07

+3
-3
-3
CHO2 1.9e-06

+3
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775


Motif 3 in BLOCKS format


to BLOCKS multiple alignment processor.


Motif 3 position-specific scoring matrix


Motif 3 position-specific probability matrix






Time 504.93 secs.


P N
SUMMARY OF MOTIFS



Combined block diagrams: non-overlapping sites with p-value < 0.0001

NameCombined
p-value
   Motifs
CHO1 2.78e-04

+1
+1
+1
+1
+3
CHO2 1.80e-04

+1
-1
+3
FAS1 7.82e-14

+2
+1
+3
FAS2 1.01e-12

-3
-2
-3
+3
+3
+1
+2
ACC1 3.41e-10

-2
+1
+2
+3
-3
-3
INO1 4.42e-19

+3
+3
-2
+3
-1
-1
-1
+3
+1
+2
OPI3 1.36e-07

+2
+2
-2
+3
+2
-2
+3
-1
+1
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775

Motif summary in machine readable format.


Stopped because nmotifs = 3 reached.


CPU: nbcr5


EXPLANATION OF MEME RESULTS

The MEME results consist of:

MOTIFS

For each motif that it discovers in the training set, MEME prints the following information:


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